The oldest record of Saurosphargiformes (Diapsida) from South China could fill an ecological gap in the Early Triassic biotic recovery

Diversification following the end-Permian mass extinction marks the initiation of Mesozoic reptile dominance and of modern marine ecosystems, yet major clades are best known from the Middle Triassic suggesting delayed recovery, while Early Triassic localities produce poorly preserved specimens or have restricted diversity. Here we describe Pomolispondylus biani gen. et sp. nov. from the Early Triassic Nanzhang-Yuan’an Fauna of China assigned to Saurosphargiformes tax. nov., a clade known only from the Middle Triassic or later, which includes Saurosphargidae, and likely is the sister taxon to Sauropterygia. Pomolispondylus biani is allied to Saurosphargidae by the extended transverse processes of dorsal vertebrae and a low, table-like dorsal surface on the neural spine; however, it does not have the typical extensive osteoderms. Rather an unusual tuberous texture on the dorsal neural spine and rudimentary ossifications lateral to the gastralia are observed. Discovery of Pomolispondylus biani extends the known range of Saurosphargiformes and increases the taxic and ecological diversity of the Nanzhang-Yuan’an Fauna. Its small size fills a different ecological niche with respect to previously found species, but the overall food web remains notably different in structure to Middle Triassic and later ecosystems, suggesting this fauna represents a transitional stage during recovery rather than its endpoint.

• *_log.out: plain text logfile output from the whole script and from each analysis with recon structed apomorphies. • *_trees.nex: all most parsimonious trees resulting from the tree search. • *_bremer.nex and *_bootstrap.nex: strict consensus trees with support values. /mrbayes_analyses/ Scripts, input files, and output files from the bayesian inference analyses in MrBayes. methods and scripts are described below ( MrBayes Analyses). These results are sep arated into the three additional ZIP files: Cheng_etal_analysis [1,2,3]_mrbayes.zip. Files include: • Analysis*.nex: MrBayes formatted NEXUS files used to build the analysis runfile.
• nexus-*.nex: NEXUS file used to run the MrBayes analysis with either gamma or lognormal model. • submission_script.sh: Bash script used to submit to BluePebble HPC.
• mb-*.sh: Bash scripts to start the BluePebble HPC analysis for the two models. • *-gamma-infinity-out and *-lnorm-infinity-out: plain text log files output from each analysis with the convergence statistics and steppingstone analysis results. • *.con.tre: majorityrule consensus tree with support values resulting from each analysis.
Modifications to Matrix of Li et al. (2014) The matrix of Li et al. (2014) was modified in two characters: • Character 102: state 2 corrected from previously state 3.
-Proximal curve of the dorsal rib is (0) smooth; (1) with slight crest developed; (2) with developed articular surface for the centrum; (3) with distinct, fanshaped uncinate process at the flange or spinous process on the concave edge.
The matrix was also coded for three additional OTUs: Pomolispondylus biani gen. et sp. nov., Hano saurus, and Hupehsuchia.
Summary statistics for each analysis are shown in supplemental tbl. S2. Resulting strict con sensus trees are shown in supplemental figs S1-S3.

MrBayes Analyses
We also analysed the same three matrices in a Bayesian inference framework implemented in MrBayes version 3.2.7a and run on the BluePebble cluster at the University of Bristol (Advanced Computing Research Centre). For each analysis we tested between two models of rate evolution (with gamma-and lognormaldistributions) using marginal likelihoods calculated by stepping stone analysis (Xie et al., 2011) following the primary tree search (supplemental figs S4, S6, S8, S10). A symmetrical Dirichlet distribution fixed at infinity was used as the prior for all analyses. For each run, commands were added in a mrbayes block by a custom Python script, and analyses were run on the University of Bristol BluePebble cluster. Convergence was assessed by reaching both estimated sample size > 200 and potential scale reduction factor approaching 1.0 (supple mental tbl. S3), as well as visually checking the trace plots with the R version 4.1.0 (R Core Team, 2021) and the package CODA version 0.19.4 (supplemental figs S5, S7, S9, S11, S13, S15) (Plummer et al., 2006). Each analysis had the following steps: Each of the NEXUS files are included in subfolders within mrbayes_analyses, with a bash submission script (for SLURM submission system) in mrbayes_analyses/submission_script.sh, which calls subordinate submission scripts in each analysis subfolder.
The following example R code was used to plot each analysis trace.

Table S3
Summary convergence statistics for analyses 1-3 in MrBayes each with a gamma-and lognormal distribution model of rate evolution. Convergence is indicated by the average standard deviation of split frequencies (ASDF) approaching 0.0 (the run is stopped at ASDF < 0.007), the estimated sample size (ESS) exceeding 200, and average potential scale reduction factor (PSRF) approaching 1.0. ASDF is a measure of the recovery of each split in the tree topology was recovered in the MCMC analysis. ESS and PSRF summarize parameters of the model (tree length for both models; alpha for gamma distribution; sigma for lognormal distribution The following marginal likelihood values (supplemental tbl. S4) resulted from each stepping stone analysis. Model selection uses the categories defined by Kass & Raftery (1995). In each case there is not enough evidence to prefer one model over the other, although gammadistributed rates of evolution are generally preferred. Resulting topologies from the six MrBayes runs (three analyses each with two rates models) are shown in supplemental figs S4, S6, S8, S10, S12, S14. Trace plots of the main parameters for each of these six runs are included in supplemental figs S5, S7, S9, S11, S13, S15.

Character lists
Character lists for the phylogenetic matrices are included here. Note that in TNT character num bers begin from 0.
These 24 character states were replaced with uncertain in marine taxa in analysis 3 following

Reconstructed apomorphies
The apomorphies below are common to the most parsimonious trees found for each analysis in TNT.

Analysis 1
Synapomorphies common to 2 trees (Node numbers refer to nodes in consensus) Ancestor : All trees: No autapomorphies:   Figure